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AlexandrovLab / SigProfilerSingleSample

SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
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DBS and ID mutational signatures? #2

Closed timchu90 closed 4 years ago

timchu90 commented 4 years ago

Hi, Thanks for your work on this program. I've successfully run this for SBS mutational signatures on my dataset and was wondering.. How do I get results for DBS and ID mutational signatures?

Thanks, Tim

marcos-diazg commented 4 years ago

Hi @timchu90,

Many thanks for your question and sorry for the late answer. You can actually run SigProfilerSingleSample for DBS and ID mutation contexts, as well as using other custom contexts. In this case you need to provide sig_database argument to single_sample function as a pandas dataframe and follow the indications in the function definition. Please find them below:

sig_database: dataframe. This is signature catalogue where the row index will be the names
of mutations and the column names will be the signature names. The sum of each column
should be one. The row numbers should be equal to the row the number of the mutational
catalogue and the order/sequence of the mutation types should be same as of those in the
mutational catalogue.

Hope this helps and thank you again for your interest,

Marcos